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HMMER

Install hidden markov model sequence analysis tools.

The HMMER tools are described here: http://hmmer.janelia.org/

Pre-compiled packages are available on the same site for pretty much any platform (also Mac OSX, Ubuntu package: hmmer). If you want to install from source, follow these steps:

wget ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz
tar zxvf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2

./configure
make
make check
sudo make install

The Biskit/Hmmer module calculates conservation scores after hmm-aligning the sequence in the PDB to a Pfam alignment. It hence also needs the Pfam database:


Usage:
see Hmmer and PDBDope.addConservation()
Custom configuration:

see

  • biskit/external/defaults/exe_hmmalign.dat
  • biskit/external/defaults/exe_hmmfetch.dat
  • biskit/external/defaults/exe_hmmindex.dat
  • biskit/external/defaults/exe_hmmpfam.dat